Transfer Ribonucleic Acids

Zachau, Hans G.

doi:10.1002/anie.196907111

Cited by 197 publications

(37 citation statements)

References 194 publications

(8 reference statements)

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“…The mixture of tRNAs should approximate a ribosomal RNA in that the double-helical regions present a.t pH 7 will vary in base composition from mostly A*U to mostly G*C, although the tRNAs sequenced to date seem to have helical regions of limited length (4 to 7 base pairs). There are apparently few long stretches of (A,G) residues (Zachau, 1969). Thus, the absence of hysteresis in the titration of unfractionated E. coli tRNA is indirect evidence that long purine stretches may underlie the longlived metastability in rRNA.…”

Section: (C) Metastable Quanine -Gumande Structures May Underlie the Hymentioning

confidence: 99%

Metastable secondary structures in ribosomal RNA molecular hysteresis in the acid-base titration of Escherichia coli ribosomal RNA

Revzin

Neumann

Katchalsky

1973

Journal of Molecular Biology

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The metastable conformational states which underlie the hysteresis displayed by Escherichia coli ribosomal RNA in its pH titration in the acid range have been analyzed in terms of acid-stable RNA secondary structures. Sedimentation measurements show that the phenomenon is ktramolecular, so that analysis of the hysteresis loops can, in principle, reveal details of molecular architecture. Hysteresis cycles obtained spectrophotometrically and potentiometrically were compared for RNA in solutions of different ionic strengths and ionic compositions. The effect is much smaller at lower ionic strength and disappears in the absence of magnesium ions. The curve followed upon addition of acid appears to reflect the equilibrium state of the system at each pH value. On the "base branch" of the loop, a slow absorbance change (complete in hours) was observed after the pH was raised by addition of a portion of base. This slow process is attributed to the annealing of "mismatched" multihelical regions of the ribosomal RNA. Certain regions, however, remain in metastable configurations for days and it is these long-lived non-equilibrium structures that underlie the hysteresis. Titration at 35°C gave hysteresis loops of the same size and shape as at 20°C ; indeed, we found that the metastabilities are not removed even at 80°C. Ultraviolet light absorbance difference spectra at 80°C between solutions at the same pH, but on different branches of the cycle, give insight into the nature of the metastable conformation(s).Our experimental observations lead us to propose that the hysteresis is due to the formation at acidic pH of double-helical structures involving protonated guanine and adenine base pairs. The G.G pairs seem especially important to account for the very high thermal stability, as well as for the fact that the structures formed at a given pH value as acid is added dissociate only at higher pH values when the solution is titrated with base. Titrations of transfer RNA, along with literature data on 16 S rRNA primary structure, imply that the metastable regions in rRNA may consist of perhaps 10 to 15 base pairs.

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Section: (C) Metastable Quanine -Gumande Structures May Underlie the Hymentioning

confidence: 99%

Metastable secondary structures in ribosomal RNA molecular hysteresis in the acid-base titration of Escherichia coli ribosomal RNA

Revzin

Neumann

Katchalsky

1973

Journal of Molecular Biology

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“…Of the specific tRNAs that have been studied, only those which read a codon on the mRNA beginning with U (uridine) contain a cytokinin, and in those tRNAs which have been sequenced, the cytokinin is located adjacent to the anticodon on the 3'-side (24,29,30,34). There (28), van Onckelen et al (32), and Fox et al (13,14) reported the incorporation of cytokinins into sRNA although the purity of some of the sRNA was later questioned by Key (19).…”

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confidence: 99%

The Mode of Incorporation of 6-Benzylaminopurine into Tobacco Callus Transfer Ribonucleic Acid

et al. 1974

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“…This methylated base is found in different tRNAs, e. g. tRNAI1e (yeast), tRNAPhe (yeast) and tRNAVa1 (yeast). These tRNAs have just one N,-methyladenine and according to the clover-leaf model, this base is in a single stranded region [30]. Nl-Methyladenine may be involved in the tertiary structure of tRNA, by pairing with adenine and by modifying the electrostatic repulsions of phosphate charges, also this base may interfere in the interactions with proteins.…”

Section: Discussionmentioning

confidence: 99%

A Study of Methylated Polyadenylic Acid

Thrierr¹,

Leng²

1971

European Journal of Biochemistry

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Copolymers with different contents of adenine and N,-methyl adenine residues have been studied, polyadenylic acid being methylated by dimethylsulfate. Thermal stability, circular dichroism and light scattering measurements are in favor of a two-strand structure a t neutral pH. Thermal stability of these products is much less sensitive to ionic strength than that of most polynucleotides, and in some cases independent of ionic strength. These copolymers interact or not with poly(U), depending on the percentage of N,-methyl adenine residues. Copolymers with high contents of methyladenine interact with poly(A) at neutral pH. These copolymers do not bind DNA-dependent RNA polymerase. Some results a t acid pH are also reported.A large number of studies have been devoted to solutions of synthetic polynucleotides in order to understand their physical properties and also because they may be considered as model molecules for deoxyribonucleic acid (DNA). We are interested, in the laboratory, by the properties of chemically methylated DNA [1,2]. Alkylating reagents react with DNA and give rise to physical and biological changes (see reviews [3-51. On the other hand, methylated bases are largely found in natural nucleic acids and their functions are still obscure. For these reasons and in order to explain some results that we found on methylated DNA [2], studies have been carried out with samples of polyadenylic acid, poly(A), which had reacted with dimethyl sulfate. Despite the fact that sites of the reaction are different in native DNA and poly(A), some interesting comparisons are possible [ 21. MATERIAL AND METHODSPolyadenylic Acid Polyadenylic acid was purchased from Miles Chemical Company. After several treatments with phenol, the product was fractionnated in 3 fractions according to the method of Eisenberg and Felsenfeld [6]. Each fraction was dialysed against 0.01 M EDTA, then exhaustively against distilled water and lyophilized. The first fraction was used in this work. MethylationWe used the method of Michelson and GrunbergManago Enzyme. DNA-dependent RNA polymerase (EC 2.7.7.6).(4 mg/ml) were added 0.16 ml tri-n-butylamine and 0.05 ml dimethyl sulfate; the solution was shaken a t 4" for different times (from 5min to 48 h, the amount of methylated adenine residues depends upon the time of reaction). At the termination of the reaction 0.05 ml M cacodylate buffer pH 7 was added; the solution was treated with ether (3 times), dialysed against 0.1 M NaC1, 0.05 M sodium cacodylate, then against distilled water and lyophilized.Methylation occurs in the Nl position of adenine, as shown by identification in the acid hydrolysate (1 N HC1, 100" for 1 h). The hydrolysate was chromatographed in the solvent system n-butanol-NH,OH 6 N (180 : 30, v/v) and only two spots were observed (adenine and Nl-methyl adenine) [8]; in the solvent system isopropanol -concentrated HC1-H,O (170 :41: 39, v/v/v) adenine and Nl-methyl adenine have the same mobility [9], and no other spot was found. The relative percentage of adenine and Nl-methyl a...

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Transfer Ribonucleic Acids

Cited by 197 publications

References 194 publications

Metastable secondary structures in ribosomal RNA molecular hysteresis in the acid-base titration of Escherichia coli ribosomal RNA

Metastable secondary structures in ribosomal RNA molecular hysteresis in the acid-base titration of Escherichia coli ribosomal RNA

The Mode of Incorporation of 6-Benzylaminopurine into Tobacco Callus Transfer Ribonucleic Acid

A Study of Methylated Polyadenylic Acid

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